chr1-20092847-G-T

Variant names:

• chr1-20092847-G-T
• rs622450

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.904 in 152,316 control chromosomes in the GnomAD database, including 62,400 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.90 (62400 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137516 AN: 152198 Hom.: 62337 Cov.: 33

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.908

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.904 AC: 137638 AN: 152316 Hom.: 62400 Cov.: 33 AF XY: 0.905 AC XY: 67374 AN XY: 74480

African (AFR) AF: 0.975 AC: 40533 AN: 41576

American (AMR) AF: 0.916 AC: 14011 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3089 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5185 AN: 5188

South Asian (SAS) AF: 0.939 AC: 4533 AN: 4830

European-Finnish (FIN) AF: 0.871 AC: 9236 AN: 10602

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58032 AN: 68024

Other (OTH) AF: 0.909 AC: 1921 AN: 2114

Alfa AF: 0.869 Hom.: 28699

Bravo AF: 0.910

Asia WGS AF: 0.976 AC: 3392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.36
PhyloP100		-0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs622450; hg19: chr1-20419340;